Variant report

Variant	rs17249138
Chromosome Location	chr19:38355880-38355881
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 55 )
Associated
traits (count: 14 )

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs1048505	0.91[ASN][1000 genomes]
rs12150862	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12151082	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12151156	0.91[ASN][1000 genomes]
rs1643455	1.00[CHB][hapmap]
rs1643459	1.00[CHB][hapmap]
rs17248097	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17248670	0.82[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17249336	0.92[CEU][hapmap];1.00[CHB][hapmap];0.85[GIH][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap];0.88[YRI][hapmap];0.84[AMR][1000 genomes]
rs17306900	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];0.84[TSI][hapmap];0.80[AMR][1000 genomes];0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2385005	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs3859549	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4536583	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4614853	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs55681348	0.86[ASN][1000 genomes]
rs55743020	0.91[ASN][1000 genomes]
rs55752822	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs55813548	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs55974157	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs55983118	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs56080901	0.83[AMR][1000 genomes]
rs56184201	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56207124	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs56230664	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs56233644	0.81[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56246446	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs56268127	0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56290614	0.81[AFR][1000 genomes];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56300335	0.83[AMR][1000 genomes]
rs56351266	0.80[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs56676595	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6508755	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap]
rs705501	1.00[CHB][hapmap]
rs7245855	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];0.84[TSI][hapmap];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7257266	0.80[AMR][1000 genomes]
rs7258011	0.83[AMR][1000 genomes]
rs73027472	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs73027480	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs73034922	0.80[AMR][1000 genomes]
rs73039029	0.91[ASN][1000 genomes]
rs73041006	0.80[AMR][1000 genomes];0.80[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs73041036	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7343065	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs8100199	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs8100684	0.80[YRI][hapmap]
rs8110293	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs833905	1.00[CHB][hapmap]
rs833919	1.00[CHB][hapmap]
rs833920	1.00[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949296	chr19:38034722-38763140	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
2	nsv833820	chr19:38190721-38414049	Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Active TSS Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
3	nsv1062040	chr19:38294465-38370456	Active TSS Enhancers Flanking Active TSS ZNF genes & repeats Weak transcription Bivalent/Poised TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
4	esv1832898	chr19:38341754-38362792	Active TSS Bivalent/Poised TSS ZNF genes & repeats Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
5	esv1825275	chr19:38341754-38376485	Enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Active TSS Active TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
6	nsv960836	chr19:38355208-38370306	Weak transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:14)

SNP	Gene	Cis/trans	Tissue	Source
rs17249138	AC012309.5	cis	Esophagus Muscularis	GTEx
rs17249138	ARHGEF1	cis	cerebellum	SCAN
rs17249138	TRAPPC6A	cis	cerebellum	SCAN
rs17249138	KIAA0961	cis	multi-tissue	Pritchard
rs17249138	AC012309.5	cis	Esophagus Mucosa	GTEx
rs17249138	AC012309.5	cis	Artery Tibial	GTEx
rs17249138	AC012309.5	cis	Thyroid	GTEx
rs17249138	AC012309.5	cis	Heart Left Ventricle	GTEx
rs17249138	HKR1	cis	multi-tissue	Pritchard
rs17249138	ZNF781	cis	Thyroid	GTEx
rs17249138	C19orf61	cis	cerebellum	SCAN
rs17249138	AC012309.5	cis	Muscle Skeletal	GTEx
rs17249138	PLEKHG2	cis	cerebellum	SCAN
rs17249138	ZNF226	cis	cerebellum	SCAN

Chromatin state (count:14 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:38347400-38356600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr19:38347400-38358000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
3	chr19:38350600-38356800	Enhancers	Fetal Brain Male	brain
4	chr19:38355200-38356800	Enhancers	HUES6 Cell Line	embryonic stem cell
5	chr19:38355200-38359000	Enhancers	iPS-15b Cell Line	embryonic stem cell
6	chr19:38355400-38356200	Enhancers	ES-I3 Cell Line	embryonic stem cell
7	chr19:38355400-38356200	Enhancers	HUES64 Cell Line	embryonic stem cell
8	chr19:38355400-38356800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
9	chr19:38355600-38356200	Enhancers	H9 Cell Line	embryonic stem cell
10	chr19:38355600-38356800	Enhancers	iPS-18 Cell Line	embryonic stem cell
11	chr19:38355600-38356800	Enhancers	NHEK	skin
12	chr19:38355600-38357200	Enhancers	HUES48 Cell Line	embryonic stem cell
13	chr19:38355800-38356000	Enhancers	iPS-20b Cell Line	embryonic stem cell
14	chr19:38355800-38356800	Enhancers	ES-WA7 Cell Line	embryonic stem cell

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